You should make all you moves from within the iTunes interface. Never in the Finder. iTunes could lose the link. iTunes is a data base manager. If moves are made outside of the iTunes interface then the move might not have been recognized.
I have always use the iTunes prefs>Advanced>copy and keep options since these became available and have rarely 'lost' an association.
If I have files on the Desktop, I use iTunes to copy them into iTunes and then delete the Desktop copy so I don't have dups. You can drag into iTunes or use File>Add to Library option to get files into iTunes.